Description

A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

icounts (file)

Internal format for dumping binary single chrs. Useful for ANGSD contamination

*.icnts.gz

hapmap_file (file)

A list of variable sites to look for heterozygosity.

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

txt (file)

Contamination estimation output.

*.txt
maintainer
Github user jbv2
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Tools

angsd
GPL v3 MIT

ANGSD: Analysis of next generation Sequencing Data

http://www.popgen.dk/angsd https://github.com/ANGSD/angsd 10.1186/s12859-014-0356-4